One of the identified threats that has currently affected up to 30% of more than 20 species of coral in Mexico is the Stony Coral Tissue Loss Disease (SCTLD), also known as the Hard Coral Tissue Loss Disease, registering the first sightings of the disease in Florida in 2014 and subsequently in other regions such as the Mexican Caribbean in 2018. The disease has spread along its 450 km of coastline, killing thousands of colonies. More than 90% of the pillar corals have disappeared, bringing them to the brink of local extinction. During summer 2019, the disease was reported in northern Belize, confirming its spread in the MAR. This new disease requires urgent action to reduce stressors, adopt better management practices, and explore innovative rescue techniques.

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SCTLD is contagious between individual corals and between coral species but does not affect humans. It is waterborne and can also be spread through contact. Research is being conducted to determine the pathogens involved and, although none have been determined yet, applications of the antibiotic amoxicillin have halted disease progression in laboratory and field experiments, so it is highly likely that there is a bacterial component.

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In September 2020 the first case of SCTLD was registered in Honduras, specifically in the island of Roatan. With the support of HRI, efforts have been made to identify the presence of this disease in other parts of Honduras such as Guanaja and Cayos Cochinos, and up to that time the disease had not been identified in other places.

As part of these efforts, a legal document was issued to the Honduran authorities by different organizations involved in the environmental management of coral reef ecosystems and Marine Protected Areas to support management and research actions in areas affected by the appearance of the Stony Coral Tissue Loss Disease, and Ministerial Agreement No 151-2020 was issued, declaring a state of marine emergency and defining the guidelines to address the emergency.

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Considering that the presence of SCTLD in the Bay Islands coral reefs is an imminent reality, the Cayos Cochinos Foundation in 2020-2021 has implemented monitoring at a site within the Cayos Cochinos Archipelago Marine Natural Monument (CACMNM), observing a possible case in January 2021 in a colony of D. Cylindrus (DCYL) which after a photographic review by international experts was estimated that it was not an infected colony. From mid-2021 to the present, the Cayos Cochinos Foundation has received the collaboration of the GCFI/NOAA Coral Reef Conservation Program to expand monitoring to other sites that have not been visited and to implement the treatment protocol for the confirmed colonies, as well as to establish management strategies to minimize the impact on the reefs in Cayos Cochinos and the involvement of other key actors in the Protected Area.